the fasta2camsa_points error

[Hemaprasanth24]

hi, I was using camsa to assemble bacterial scafflods to a chromosome the fasta2camsa.py has ran successfully by the assembly_points are empty (camsa) hema@hema-Aspire-A715-51G:~/camsa$ fasta2camsa_points.py assembly1.fasta assembly2.fasta assembly3.fasta assembly4.fasta assembly5.fasta assembly6.fasta assembly7.fasta assembly8.fasta assembly9.fasta assembly10.fasta assembly11.fasta assembly12.fasta assembly13.fasta assembly14.fasta assembly15.fasta assembly16.fasta assembly17.fasta assembly18.fasta assembly19.fasta assembly20.fasta assembly21.fasta assembly22.fasta assembly23.fasta assembly24.fasta assembly25.fasta assembly26.fasta assembly27.fasta assembly28.fasta assembly29.fasta assembly30.fasta assembly31.fasta assembly32.fasta assembly33.fasta assembly34.fasta assembly35.fasta assembly36.fasta assembly37.fasta assembly38.fasta assembly39.fasta assembly40 -o output

Sergey Aganezov & Max A. Alekseyev (c)		Computational Biology Institute, The George Washington University
Converting FASTA formatted scaffolding results for further CAMSA processing.
For more information refer to github.com/compbiol/camsa/wiki
With any questions, please, contact Sergey Aganezov [aganezov(at)cs.jhu.edu]

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Command Line Args: assembly1.fasta assembly2.fasta assembly3.fasta assembly4.fasta assembly5.fasta assembly6.fasta assembly7.fasta assembly8.fasta assembly9.fasta assembly10.fasta assembly11.fasta assembly12.fasta assembly13.fasta assembly14.fasta assembly15.fasta assembly16.fasta assembly17.fasta assembly18.fasta assembly19.fasta assembly20.fasta assembly21.fasta assembly22.fasta assembly23.fasta assembly24.fasta assembly25.fasta assembly26.fasta assembly27.fasta assembly28.fasta assembly29.fasta assembly30.fasta assembly31.fasta assembly32.fasta assembly33.fasta assembly34.fasta assembly35.fasta assembly36.fasta assembly37.fasta assembly38.fasta assembly39.fasta assembly40 -o output Config File (/home/hema/anaconda3/envs/camsa/lib/python3.9/site-packages/camsa/logging.ini): c-logging-level: 20 c-logging-formatter-entry:%(asctime)s - %(name)-15s - %(levelname)-7s - %(message)s Config File (/home/hema/anaconda3/envs/camsa/lib/python3.9/site-packages/camsa/utils/fasta/fasta2camsa_points.ini): c-cov-threshold: 90.0 c-coords-pairs-strategy:mid-point-sort nucmer-cli-arguments:--maxmatch -c 100 nucmer-path: nucmer show-coords-cli-arguments:-r -c -l show-coords-path: show-coords delta-filter-cli-arguments:-r -q delta-filter-path: delta-filter Defaults: --ensure-all: False

2023-09-20 12:32:50,137 - CAMSA.utils.fasta2camsa_points - INFO - Starting the converting process 2023-09-20 12:32:50,137 - CAMSA.utils.fasta2camsa_points - INFO - Working with "assembly2.fasta" 2023-09-20 12:32:50,137 - CAMSA.utils.fasta2camsa_points - INFO - Running NUCmer for "assembly2.fasta" scaffolds file, using "assembly1.fasta" as query. This might take time. 2023-09-20 12:32:50,137 - CAMSA.utils.fasta2camsa_points - INFO - nucmer --maxmatch -c 100 -p /home/hema/camsa/output/fasta2camsa/assembly2 assembly2.fasta assembly1.fasta > /home/hema/camsa/output/fasta2camsa/logs/nucmer_assembly2.stdout.txt 2> /home/hema/camsa/output/fasta2camsa/logs/nucmer_assembly2.stderr.txt 2023-09-20 12:32:50,199 - CAMSA.utils.fasta2camsa_points - INFO - NUCmer finished running for "{scaffolds_file}" scaffolds file. 2023-09-20 12:32:50,199 - CAMSA.utils.fasta2camsa_points - INFO - Running delta-filter util for "/home/hema/camsa/output/fasta2camsa/assembly2.delta" file. 2023-09-20 12:32:50,199 - CAMSA.utils.fasta2camsa_points - INFO - delta-filter -r -q /home/hema/camsa/output/fasta2camsa/assembly2.delta > /home/hema/camsa/output/fasta2camsa/assembly2.filtered.delta 2> /home/hema/camsa/output/fasta2camsa/logs/delta_filter_assembly2.stderr.txt 2023-09-20 12:32:50,201 - CAMSA.utils.fasta2camsa_points - INFO - delta-filter util has finished running for "/home/hema/camsa/output/fasta2camsa/assembly2.delta" 2023-09-20 12:32:50,201 - CAMSA.utils.fasta2camsa_points - INFO - Running show-coords util for "/home/hema/camsa/output/fasta2camsa/assembly2.filtered.delta" file. 2023-09-20 12:32:50,201 - CAMSA.utils.fasta2camsa_points - INFO - show-coords -r -c -l /home/hema/camsa/output/fasta2camsa/assembly2.filtered.delta > /home/hema/camsa/output/fasta2camsa/assembly2.coords 2> /home/hema/camsa/output/fasta2camsa/logs/show_coords_assembly2.stderr.txt 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - show-coords util has finished running for "/home/hema/camsa/output/fasta2camsa/assembly2.filtered.delta". 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - Parsing "/home/hema/camsa/output/fasta2camsa/assembly2.coords". 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - Writing coords data in terms of CAMSA assembly points in "/home/hema/camsa/output/assembly2.camsa.points" 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - Finished converting data for "assembly2" 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - Working with "assembly3.fasta" 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - Running NUCmer for "assembly3.fasta" scaffolds file, using "assembly1.fasta" as query. This might take time. 2023-09-20 12:32:50,204 - CAMSA.utils.fasta2camsa_points - INFO - nucmer --maxmatch -c 100 -p /home/hema/camsa/output/fasta2camsa/assembly3 assembly3.fasta assembly1.fasta > /home/hema/camsa/output/fasta2camsa/logs/nucmer_assembly3.stdout.txt 2> /home/hema/camsa/output/fasta2camsa/logs/nucmer_assembly3.stderr.txt 2023-09-20 12:32:50,243 - CAMSA.utils.fasta2camsa_points - INFO - NUCmer finished running for "{scaffolds_file}" scaffolds file. 2023-09-20 12:32:50,243 - CAMSA.utils.fasta2camsa_points - INFO - Running delta-filter util for "/home/hema/camsa/output/fasta2camsa/assembly3.delta" file. 2023-09-20 12:32:50,243 - CAMSA.utils.fasta2camsa_points - INFO - delta-filter -r -q /home/hema/camsa/output/fasta2camsa/assembly3.delta > /home/hema/camsa/output/fasta2camsa/assembly3.filtered.delta 2> /home/hema/camsa/output/fasta2camsa/logs/delta_filter_assembly3.stderr.txt 2023-09-20 12:32:50,246 - CAMSA.utils.fasta2camsa_points - INFO - delta-filter util has finished running for "/home/hema/camsa/output/fasta2camsa/assembly3.delta" 2023-09-20 12:32:50,246 - CAMSA.utils.fasta2camsa_points - INFO - Running show-coords util for "/home/hema/camsa/output/fasta2camsa/assembly3.filtered.delta" file. 2023-09-20 12:32:50,246 - CAMSA.utils.fasta2camsa_points - INFO - show-coords -r -c -l /home/hema/camsa/output/fasta2camsa/assembly3.filtered.delta > /home/hema/camsa/output/fasta2camsa/assembly3.coords 2> /home/hema/camsa/output/fasta2camsa/logs/show_coords_assembly3.stderr.txt